Next Article in Journal
Genomic Analysis of Antimicrobial Resistance and Resistance Plasmids in Salmonella Serovars from Poultry in Nigeria
Next Article in Special Issue
Potential Target Site for Inhibitors in MLSB Antibiotic Resistance
Previous Article in Journal
Incorporation of Hybrid Nanomaterial in Dental Porcelains: Antimicrobial, Chemical, and Mechanical Properties
Previous Article in Special Issue
The Prospect of Repurposing Immunomodulatory Drugs for Adjunctive Chemotherapy against Tuberculosis: A Critical Review
Open AccessArticle

Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Hub Genes Associated with Mycobacterial Infection of Human Macrophages

by 1,2,*,†, 3,†, 4, 5 and 2,*
1
College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China
2
Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, 08290 Cerdanyola del Vallès, Spain
3
Laboratory of Omics Technology and Bioinformatics, West China Hospital, Sichuan University, Chengdu 610017, China
4
Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London WC1E 7HX, UK
5
Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PX, UK
*
Authors to whom correspondence should be addressed.
These authors have contributed equally to this work.
Academic Editor: John E. Gustafson
Received: 28 November 2020 / Revised: 28 December 2020 / Accepted: 14 January 2021 / Published: 20 January 2021
Tuberculosis (TB) is still a leading cause of death worldwide. Treatments remain unsatisfactory due to an incomplete understanding of the underlying host–pathogen interactions during infection. In the present study, weighted gene co-expression network analysis (WGCNA) was conducted to identify key macrophage modules and hub genes associated with mycobacterial infection. WGCNA was performed combining our own transcriptomic results using Mycobacterium aurum-infected human monocytic macrophages (THP1) with publicly accessible datasets obtained from three types of macrophages infected with seven different mycobacterial strains in various one-to-one combinations. A hierarchical clustering tree of 11,533 genes was built from 198 samples, and 47 distinct modules were revealed. We identified a module, consisting of 226 genes, which represented the common response of host macrophages to different mycobacterial infections that showed significant enrichment in innate immune stimulation, bacterial pattern recognition, and leukocyte chemotaxis. Moreover, by network analysis applied to the 74 genes with the best correlation with mycobacteria infection, we identified the top 10 hub-connecting genes: NAMPT, IRAK2, SOCS3, PTGS2, CCL20, IL1B, ZC3H12A, ABTB2, GFPT2, and ELOVL7. Interestingly, apart from the well-known Toll-like receptor and inflammation-associated genes, other genes may serve as novel TB diagnosis markers and potential therapeutic targets. View Full-Text
Keywords: mycobacterium; macrophage; WGCNA; transcriptome; network analysis mycobacterium; macrophage; WGCNA; transcriptome; network analysis
Show Figures

Figure 1

MDPI and ACS Style

Lu, L.; Wei, R.; Bhakta, S.; Waddell, S.J.; Boix, E. Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Hub Genes Associated with Mycobacterial Infection of Human Macrophages. Antibiotics 2021, 10, 97. https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics10020097

AMA Style

Lu L, Wei R, Bhakta S, Waddell SJ, Boix E. Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Hub Genes Associated with Mycobacterial Infection of Human Macrophages. Antibiotics. 2021; 10(2):97. https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics10020097

Chicago/Turabian Style

Lu, Lu; Wei, RanLei; Bhakta, Sanjib; Waddell, Simon J.; Boix, Ester. 2021. "Weighted Gene Co-Expression Network Analysis Identifies Key Modules and Hub Genes Associated with Mycobacterial Infection of Human Macrophages" Antibiotics 10, no. 2: 97. https://0-doi-org.brum.beds.ac.uk/10.3390/antibiotics10020097

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Search more from Scilit
 
Search
Back to TopTop